NM_139281.3:c.26C>A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_139281.3(WDR36):c.26C>A(p.Thr9Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000315 in 1,614,102 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_139281.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDR36 | ENST00000513710.4 | c.26C>A | p.Thr9Lys | missense_variant | Exon 1 of 23 | 1 | NM_139281.3 | ENSP00000424628.3 | ||
WDR36 | ENST00000505303.5 | n.162C>A | non_coding_transcript_exon_variant | Exon 1 of 15 | 5 | |||||
WDR36 | ENST00000515784.1 | n.136C>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000223 AC: 34AN: 152238Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000179 AC: 45AN: 251064Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135790
GnomAD4 exome AF: 0.000325 AC: 475AN: 1461864Hom.: 0 Cov.: 31 AF XY: 0.000308 AC XY: 224AN XY: 727234
GnomAD4 genome AF: 0.000223 AC: 34AN: 152238Hom.: 0 Cov.: 33 AF XY: 0.000161 AC XY: 12AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.194C>A (p.T65K) alteration is located in exon 1 (coding exon 1) of the WDR36 gene. This alteration results from a C to A substitution at nucleotide position 194, causing the threonine (T) at amino acid position 65 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at